[BioC] Phylogenetic inference

[Ramon Diaz]

Dear Kjetil and Susan,

I am not sure about the functionalities but the "ape" program in CRAN might do 
some of what you want. With regards to PHYLOGR, no, it won't do phylogenetic 
inference ---it is targeted for the statistical analysis of data in a 
phylogenetic context, but phylogenies are to be given to PHYLOGR. Right now 
PHYLOGR will not work on the latest R version because of a few silly things 
that I have not had time to fix yet (I am the maintainer).

For other programs, you might want to take a look at Joe Felsenstein's list of 
software
http://evolution.genetics.washington.edu/phylip/software.html

Best,

Ramón




On Friday 17 January 2003 02:10, Susan Holmes wrote:
> Dear Kjetil,
> I have done alot of phylogeny studies using
> phylip that I interface with R using RSPython.
> There is alos a package that is called phylogr
> in R, but it doesn't do traditional phylogeny.
> I would actually be interested in collaborating on
> rewriting some of the phylogeny programs IN R.
>
> Best
> Susan Holmes
> Statistics
> Stanford
>
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******** Original query by K. Halvorsen **********************
On Friday 17 January 2003 00:57, kjetil brinchmann halvorsen wrote:
> Hola!
>
> We have some sequencing data, from amazonian fishes,
> which only covers "dna basura", so no genes. The goal
> is phylogenetic inference.
>
> Is Bioconductor usefull for this, or are there other R
> packages/ other software on the net?
>
> Kjetil Halvorsen
>
-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
http://bioinfo.cnio.es/~rdiaz